File Coverage

blib/lib/Bio/MUST/Apps/TwoScalp/AlignAll.pm

Criterion	Covered	Total	%
statement	24	33	72.7
branch			n/a
condition			n/a
subroutine	8	9	88.8
pod	0	1	0.0
total	32	43	74.4

package Bio::MUST::Apps::TwoScalp::AlignAll;
# ABSTRACT: internal class for two-scalp tool
# CONTRIBUTOR: Amandine BERTRAND <[e-mail]>
$Bio::MUST::Apps::TwoScalp::AlignAll::VERSION = '0.201810';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments '###';

#use List::AllUtils qw(part);

use Bio::MUST::Core;

use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Drivers::Mafft';


has 'file' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    required => 1,
    coerce   => 1,
);


has 'ali' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_ali',
    #handles  => qr{.*}xms,     # DO NOT WORK... WHY??
    handles  => [qw( all_seqs all_seq_ids dont_guess restore_ids store_fasta temp_fasta count_seqs)],
);


sub BUILD {
    my $self = shift;

    my $ali1 = $self->file;

    my ($filename1, $id_mapper1) = $ali1->temp_fasta( {id_prefix => 'file1-'} );

    my $mafft = Mafft->new( file => $filename1 );
    my $ali_out = $mafft->align_all;

    $ali_out->dont_guess;
    $ali_out->restore_ids($id_mapper1);

    $self->_set_ali($ali_out);

    return;
}
__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=head1 NAME

Bio::MUST::Apps::TwoScalp::AlignAll - internal class for two-scalp tool

=head1 VERSION

version 0.201810

=head1 SYNOPSIS

    # TODO

=head1 DESCRIPTION

    # TODO

=head1 AUTHOR

Denis BAURAIN <[e-mail]>

=head1 CONTRIBUTOR

=for stopwords Amandine BERTRAND

Amandine BERTRAND <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut